Host Dependent and Geographical Structuring of Citrus Canker Bacteria at
Peshawar, Pakistan
Safi Ullah1, Laila Jamshed1, Musharaf Ahmed2,
Zia-ur-Rehman1, Aamir Iqbal1, Muhammad Zakria3,
Muhammad Rameez Khan1, Mudassar Nawaz Khan1, Ijlal
Hussain4 and Sajid Ali1,5*
1Institute of Biotechnology & Genetic Engineering, The University of
Agriculture, Peshawar, Pakistan
2Department of Plant Pathology, The University of
Agriculture, Peshawar, Pakistan
3Crop Disease Research Institute, National Agricultural
Research Center, Islamabad, Pakistan
4Department of Agriculture (Extension), Gilgit-Baltistan,
Pakistan
5Department of Agriculture, Hazara University, Mansehra,
Pakistan
*For correspondence: bioscientist122@yahoo.com
Received 07 December 2020; Accepted 24 March 2021; Published 10 May
2021
Abstract
Citrus canker
disease, caused by Xanthomonas axonopodis
pv. Citri (Xac) induces huge losses to citrus, particularly in nurseries. This
study assessed the level of genetic diversity and divergence in Xac population prevalent in district
Peshawar on various host species, based on isolates collected from different
fruit nurseries of Peshawar. Surveillance resulted in collection of 80 samples,
out of which 50 bacterial samples were isolated. Genotyping of the isolates
using RAPD markers amplified 35 scorable loci with an average of 8.7 loci per
primers and level of polymorphism was 100%, i.e., almost all of the
isolates genotyped had a different multilocus genotype. The loci GLA-031000 was
recorded with the highest gene diversity (0.51) followed by GLB-05_1000 and
GLA-03_1100 (0.49). The maximum diversity index (0.50) was recorded for loci
GLA-031000, followed by GLB-051000 and GLA-03_1100 (0.48). A high diversity was observed across all
locations, with the range of genotypic diversity from 0.778 (detected at
Malakandair) to 0.955 (detected at Hayatabad and Tarnab). Divergence between
samples collected from different locations was limited as revealed by the PCA,
PCoA, phylogenetic tree and network analyses. Samples originated from various
hosts also revealed a high diversity across host types with the minimum
genotype diversity observed for Eureka Lemon (0.750) and the maximum for sweet
lemon (0.966). The divergence for samples collected on various citrus host
types was absent. The very small linkage disequilibrium (0.006–0.159) reflected
on the potential recombination in the population, which must have direct
implications to disease management and resistance exploitation. © 2021 Friends
Science Publishers
Keywords: Xanthomonas axonopodis; Molecular genotyping; Citrus orchards; Population structure
Introduction
The Citrus
genus belongs to sub-tribe Citrinae
of family Rutaceae of subfamily Aurantioidease (Araujo
et al. 2003), which originated from Monsoon areas and spread out from
Pakistan to China, India, Northwest Australia and New Guinea (Ulubelde 1985). Citrus is one the most
important of fruit crops that are widely grown in Pakistan, and the country
occupied 12th most significant position in citrus production all around the world
(Siddique and Garnevska 2018). Pakistan has a total
of 206,569 hectares of cultivated areas for citrus,
the province of Punjab has the highest citrus production i.e., 2,315895
ton on 183,210 hectares, mainly due to suitable environmental and growing
conditions (Memon 2017). The tropical, subtropical and temperate
regions with the appropriate climates like the winter temperatures and lack of
frost provide suitable environment for the citrus fruit production. In such
areas, the suitable soils and sufficient water support the citrus tree growth
as well as fruit production (Kahn et al. 2001).
Despite the
economic importance of citrus, the countrywide production is always at risk due
to diseases. Various diseases could be present on citrus, though the citrus
canker is the most common and dangerous diseases for all types of citrus crops
(Das 2003). The disease accounts for the significant losses of citrus, and the
degree of disease severity varies with pathogen type, host crop and climate
conditions (Das 2003). The disease is widespread in India, Japan, Pakistan and
other South-East Asian countries from where it has dispersed to the rest of the
world except Europe (Schubert and Miller 1996; Das 2003). Commonly, the
infection of canker pathogen does not occur in drought condition and has been
eradicated from some of such areas. Still, the extensive incidences of the
diseases in many areas pose a continuous thread to citri-culture in canker free
areas, if the pathogen invades into these areas (Das 2003). In US the disease
has been important where it did severe damages as millions of diseased trees
were cut off or burnt down (Schubert and Miller 1996).
Canker
disease symptoms are distinguished by the incidence of noticeable necrotic
lesions on leaves, foliage and fruit (Graham and Dewdney 2014). At first, the
lesions are of smaller size but later both epidermal areas become ruptured and
hyperplasia (increase in cell number) is caused by the pathogen. The circular
lesion on stems leaves and fruits rose into yellow or white soft eruptions.
These eruptions then change into light tan to brown corky canker (Schubert and
Miller 1996). Severe infection may result in defoliation, die-back, deformation
and premature fruit drop (Graham and Dewdney 2014). Canker disease causes
fruits losses due to abscission of premature fruits, or the canker lesion makes
its quality worse that is not acceptable by the fresh market in many parts of
the world, including Pakistan (Schubert and Miller 1996).
The disease is
distributed worldwide, and is important in Pakistan with different variants
prevalent in different parts of the world. The disease was first reported in
Oman in 1985. Related pathogenic isolates have been cited in Saudi Arabia, India and
Iran (Vernière et
al. 1998). There is variability in various isolates in terms of antibiotic
resistance in Reunion and islands of Indian Ocean (Graham et al. 2000).
The
phytopathogenic bacteria from the genus Xanthomonas infect wide varieties
of plants and represent great importance for citrus production (Silva et al.
2002). In specific, Xac pv. citri infects smaller
numbers of plant species and have limited host range (Leyns et al.
1984). X. axonopodis that causes Asiatic citrus canker is responsible
for significant citrus crop losses worldwide and in some countries the pathogen
has a status of quarantine organism (Gottwald et al. 2002). Xac pv. citri infects citrus
plants by wounds or stomata and attacks the plant cell with a range of different
virulence proteins transported out of the bacterial cell (Brunings and
Gabriel 2003). Both the pathogen and its host species are considered to be
originated in Asia (Civerolo 1984; Leyns et al. 1984) and thus possess a
continuous economic threat in this area.
Considering the importance of this disease, there is a
dire need to assess variability in the pathogen population in response to
various host species for a better control of the disease (Ali et al.
2017). Variability in pathogen population could be assessed based on
inoculation experiments (Schaad et al. 2001), serological tests and
molecular assays using DNA based techniques (Alvarez et al. 1991;
Gottwald et al. 1991; Sun et al. 2004). Several DNA based assays are presently being used for
assessing variability in pathogen populations for crop pathogens (Ali et al.
2017).
Among various DNA based molecular genotyping techniques,
RAPD, SSRs, and sequencing techniques are very much useful. Integrated
approach that combines bacterial isolation and conventional polymerase chain
reaction (PCR) is most powerful techniques that have been adopted for accurate,
fast and reliable detection and identification of Xac pv. citri (Shehzadi
and Naz 2019). Different sets of primers usually
designed for specific and target region of bacteria DNA to check all variations
among strains of citrus canker (Katkar et al. 2016).
The present study was designed
to assess variability in citrus canker pathogen population using RAPD markers,
while considering the role of host (type of citrus).
The objectives of the current study were; i): To assess the prevalence of
citrus canker on various citrus
ecotypes at fruit nurseries of District Peshawar. ii): to isolate and
characterize the strains of citrus canker bacteria from fruit nurseries of
district Peshawar. iii). To assess the variability in pathogen population in
relation to host considering various ecotypes of citrus. The information obtained would be useful for devising
appropriate disease management strategy, while considering the level of
pathogen diversity and divergence.
Materials and Methods
The current study was designed to assess variability in
the citrus canker pathogen population in relation to citrus host at district
Peshawar. The sampling was done at different locations of Peshawar, while the
isolation of bacteria, multiplication and genotyping was conducted at of the
Genomics and Bioinformatics Division, Institute of Biotechnology and Genetic
Engineering, The University of Agriculture Peshawar, Pakistan. Morphological
and biochemical based
diagnostic methods are available for citrus canker bacteria, but these
protocols require skilled personnel and are time consuming Population genetic
structure was studied through screening several RAPD genetic markers which
showed different diversity levels. In this study, we developed a RAPD based PCR
optimized protocol for reliable and robust differentiation of Xac pv. Citri.
Disease
surveillance and sampling
The infestation
of disease was assessed in major nurseries of citrus at District Peshawar i.e.,
UAP Campus (30 samples), Hayatabad (30 samples) and Tarnab farm (30 samples)
(Table 1). Infected leaf samples of citrus plants were collected from these
three different areas of Peshawar. Samples were appropriately collected in paper
bags and were labeled with necessary information e.g., detailed
location, host type, plant age and date of sampling. These samples were then
shifted to the lab for isolation and purification process.
Table 1: Surveillance of citrus canker bacterial infestation and
sample collection to assess diversity in citrus canker causing bacterial
population at district Peshawar
Sub-location |
Samples collected |
Samples isolated |
Samples genotyped |
UAP, nurseries |
30 |
6 |
6 |
Hayatabad nurseries |
30 |
22 |
22 |
Tarnab Farm nurseries |
30 |
22 |
22 |
Overall |
90 |
50 |
45 |
Table 2: Primers sequences and their optimized PCR thermal
profiles
Primer Name |
Gld-18 |
Gla-03 |
Gla-04 |
Sequence |
5`GAGAGCCAAC3` |
5`AGTTCAGCCAC3` |
5`AATCGGGCTG3` |
Initial denaturation |
95°C for 5 min |
95°C for 5 min |
95°C for 5 min |
Denaturation |
95°C for 30 s |
95°C for 30 s |
95°C for 30 s |
Annealing |
32°C for 45 s |
32°C for 45 s |
32°C for 45 s |
Extension |
72°C for 45 s |
72°C for 45 s |
72°C for 45 s |
PCR Cycles |
35 |
35 |
35 |
Final Extension |
72°C for 10 min |
72°C for 10 min |
72°C for 10 min |
Isolation
of bacteria from the canker lesions
Leaves with typical canker symptoms were rinsed with
distilled water and then bacterial affected part was cut with sterilized
blades. The infected part was then surface sterilized with 0.9% Mercuric
Chloride and then washed it twice with sterilized water. Dried canker lesions
were crushed in phosphate buffer solution containing 137 mM NaCl, 10 mM
phosphate, 2.7 mM KCL and pH 7.4 (Pruvost et
al. 1992). These macerates were cultured on Petri plates having nutrient
agar growth medium containing 0.5% peptone, 0.3% yeast extract, 0.5% NaCl and
1.5% agar. Also, added 16 mg cephalexin in the media for the selective
growth of canker bacteria. The plates were incubated at 28°C in incubator for 72hrs. The cultured
bacteria were purified and sub-cultured on agar growth medium. The isolates
were further cultured in nutrient agar broth for DNA extraction purpose.
Molecular
genotyping of bacterial isolates
The bacterial
suspension in nutrient broth was centrifuged at 6000 rpm for 3 min and pellet
was collected. Total genomic DNA was extracted by re-suspending the bacterial
cells in CTAB buffer containing (2% CTAB, 10
mM Tris HCl, 5 mM NaCl, 1 mM EDTA, 1% PVP and 1%
marceptoethanol) (Ali et al. 2017).
The bacterial suspension was then transferred to 1.5 mL Eppendorf tube and
incubated in water bath at 65°C for 30 min. Tubes were centrifuged at 12000 rpm
for 15 min and supernatants were transferred to fresh tube. Around 28 µL Na acetate and 750 µl Phenol:
Chloroform: Isoamyl alcohol (25:24:1) was added to supernatant and centrifuged
at 12000 rpm for 10 min to separate the phases. An upper aqueous layer was
transferred to fresh Eppendorf tube and double amount of iso-propanol was added
and centrifuged at 12000 rpm for 30 min to allow precipitation. After that, the
supernatant was discarded without disturbing the pellet and washed with 70%
ethanol through centrifugation for 7 min at 12000 rpm. The ethanol was
discarded and the pellet was air dried. Then 1 µL RNAse (10 mg/mL) and
30 µL TE (10 mM) buffer were
added to remove RNA. Extracted DNA was stored at -20°C. DNA concentration was
assessed by measuring the optical density (OD) at 260 nm using Nanodrop. The
quality of DNA was examined by gel electrophoresis.
Molecular genotyping of these isolates was done through
three RAPD primers using conventional PCR (Table 2). A PCR thermal profile was calibrated for each primer
through trying various annealing temperatures. PCR reaction mix for 10 µL
reaction was prepared for each primer in the PCR tube. It contained 2.8 µL
of water, 5 µL of PCR green master mix, 1 µL of single RAPD
primer, 0.2 µL of DNA Taq Polymerase and 1 µL of DNA sample. The
PCR tubes were placed in the PCR machine and subjected to the primer thermal
conditions. The
PCR amplified products were run on agarose gel and DNA were visualized in the gel documentation system.
Data analysis
After visualization of gel, the RAPD bands were scored for the
polymorphism of various loci, while considering their size in Table 3: Summary
statistics for RAPD markers amplified in citrus canker pathogen population from
main citrus nurseries of district Peshawar
RAPD loci |
Gene diversity |
Simpsons diversity index |
Evenness index |
GLA-04_500 |
0.27 |
0.27 |
0.67 |
GLA-04_800 |
0.25 |
0.24 |
0.64 |
GLA-04_1000 |
0.25 |
0.24 |
0.64 |
GLA-04_1100 |
0.27 |
0.27 |
0.67 |
GLA-04_1200 |
0.12 |
0.11 |
0.50 |
GLA-04_200 |
0.04 |
0.04 |
0.40 |
GLA-03_100 |
0.12 |
0.11 |
0.50 |
GLA-03_350 |
0.22 |
0.21 |
0.60 |
GLA-03_400 |
0.41 |
0.40 |
0.83 |
GLA-03_500 |
0.43 |
0.42 |
0.86 |
GLA-03_800 |
0.33 |
0.32 |
0.72 |
GLA-03_1000 |
0.51 |
0.50 |
0.99 |
GLA-03_1100 |
0.49 |
0.48 |
0.96 |
GLA-03_1200 |
0.22 |
0.21 |
0.60 |
GLA-03_1300 |
0.22 |
0.21 |
0.60 |
GLA-03_900 |
0.33 |
0.32 |
0.72 |
GLA-03_700 |
0.43 |
0.42 |
0.86 |
GLA-03_300 |
0.04 |
0.04 |
0.40 |
GLB-05_300 |
0.04 |
0.04 |
0.40 |
GLB-05_400 |
0.12 |
0.11 |
0.50 |
GLB-05_500 |
0.22 |
0.21 |
0.60 |
GLB-05_600 |
0.18 |
0.18 |
0.57 |
GLB-05_700 |
0.35 |
0.34 |
0.75 |
GLB-05_800 |
0.39 |
0.38 |
0.81 |
GLB-05_1000 |
0.49 |
0.48 |
0.96 |
GLB-05_1200 |
0.15 |
0.15 |
0.54 |
GLB-05_1300 |
0.39 |
0.38 |
0.81 |
GLB-05_1500 |
0.22 |
0.21 |
0.60 |
GLB-05_1100 |
0.33 |
0.32 |
0.72 |
GLD-018_300 |
0.43 |
0.42 |
0.86 |
GLD-018_500 |
0.22 |
0.21 |
0.60 |
GLD-018_700 |
0.35 |
0.34 |
0.75 |
GLD-018_1000 |
0.47 |
0.46 |
0.93 |
GLD-018_1300 |
0.27 |
0.27 |
0.67 |
GLD-018_600 |
0.15 |
0.15 |
0.54 |
comparison with the ladder.
Variability in frequency of various alleles was assessed for isolates
originating from various hosts in MS Excel. Population genetic analyses were
conducted in POPPR package in R software to assess population subdivision and
diversity across various hosts and sub-locations.
Results
Isolation of the pathogen associated with plant disease
is important to know the etiology and management of diseases. The focus of our
study was to find variability in citrus canker pathogen population in relation
to citrus host types at district Peshawar. The first part of the study involved
field sampling, which was done in the fruit nurseries of Malkandair fruit farm,
Hayatabad fruit nurseries and Tarnab farm fruit nurseries. Infected citrus
plants showed canker lesions on fruits and leaves. Varying level of disease
severity was observed on young plants across locations.
Our work revealed diversity and
divergence for citrus canker pathogen samples originating from various fruit
nurseries of district Peshawar. A total of 35 loci for randomly amplified
polymorphic DNA markers were amplified, which enabled to explore genetic
diversity and divergence in citrus canker bacterial population, as assessed
across locations and over different citrus host types i.e., Sweet
Orange, Sour Orange and Lemon.
Feasibility of molecular markers
For
genetic characterization, a total of 35 loci were amplified using a set of four
randomly amplified polymorphic DNA markers. The maximum number of loci (12) was recorded
for GLB-03, followed by
GLB-05 (11 loci), while GLA-04 and GLD-18 resulted in
amplification of 6 loci (Table 3). Plotting of multilocus genotypes against the
35 RAPD loci detected,
Fig. 1: Feasibility
of RAPD markers for assessment of diversity and divergence in citrus canker
pathogen population as revealed through (A)
detection of multilocus genotype against the loci
resampled, and (B) the association
among different RAPD loci
confirmed the
suitability of markers for the detection of variability in the pathogen
population of citrus canker (Fig. 1A). It revealed that addition of loci till
22–28 loci added detection of further MLGs, whereas the tested 35 loci were
able to detect all of the MLGs present in the dataset. To check the association between the amplified 35 loci, the r2
was calculated using pair wise linkage disequilibrium analysis (Fig. 1B). An
overall lack of strong linkage was evident across the amplified loci.
The maximum gene diversity (0.51) was recorded for loci GLA-03_1000, followed by
GLB-05_1000 and GLA-03_1100 (0.49), while the minimum gene diversity (0.04) was
observed for locus GLA-04_200. The maximum
diversity index (0.50) was recorded for loci GLA-03_1000, followed by GLB-05_1000 and
GLA-03_1100 (0.48), while the minimum diversity index (0.04) was observed for locus GLA-04_200, GLA-03_300 and
GLB-05_300. The maximum evenness index (0.99) was observed for GLA-03_1000 while
minimum evenness (0.40) was recorded for locus GLA-04_200, GLA-03_300 and GLB-05_300.
Divergence
and diversity across locations
Divergence of isolates sampled from different locations was assessed
through principal component analysis, principal coordinate analysis, neighbor
joining tree and network analysis. The principal component analysis considering
information on sample location, revealed a weak divergence across locations (Fig.
2A). The first component explained 11.37% of the variation while the second
component contributed 9.83%, with an overall component contribution of 21.2%
(Fig. 2A). The divergence was further elaborated by principle
coordinate analysis, where the samples from different locations were clustered
together with limited overlap across locations, particularly for the samples
from Hayatabad, which were dispersed (Fig. 2B). Interestingly, the samples from
Malakandair nursery were clearly divergent from Hayatabad, though had
overlapping with the samples from Tarnab farm nurseries. The neighbour joining
phylogenetic tree further confirmed this pattern of divergence and population
subdivision (Fig. 3A). Most of the isolates from the Hayatabad nurseries were
present on separate phylogenetic clades, while that of Tarnab farm nurseries
were grouped together, although some of the isolates were positioned on at the
clade specific to another location. The citrus canker pathogen isolates sampled
from Malakandair farm, were grouped in the middle of the clades from the two
locations (Fig. 3A). This pattern of divergence was further elucidated by the
network analyses, where multiple linking networks were possible with samples
from Malakandair positioned in the middle of network (Fig. 3B).
Fig. 2: Divergence among
citrus canker population from various locations of main citrus nurseries of
district Peshawar, as revealed by Principal component analyses (A) and Principle
co-ordinate analyses (B)
Fig. 3: Divergence
among citrus canker population from various locations of main citrus nurseries
of district Peshawar, as revealed by Neighbor-joining (NJ) tree (A) and Network Analyses (B)
An overall high diversity was estimated for the citrus canker pathogen
population sampled from various fruit nurseries of district Peshawar (Table 4).
A total of 49 MLGs was observed out of 50, samples where each isolate
represented distinct MLG, except a couple of isolates, which were identical. At
Hayatabad and Tarnab Farm, all of the genotyped isolates represented distinct
multilocus genotypes (22MLGs out of 22 samples), while at Malakandair nursery
five distinct MLGs were detected out of 6 samples (Table 4). The genotypic
diversity ranged from 0.778 (detected at Malakandair) to 0.955 (detected at
Hayatabad and Tarnab), with an overall value of 0.978 (Table 4). The maximum
gene diversity was detected at Hayatabad (0.336) and the minimum was detected
at Malkandar (0.099) with an overall diversity of 0.276,
respectively. The maximum linkage disequilibrium was observed for samples
collected from Malkandair location whereas the minimum linkage disequilibrium
was observed for samples collected from Tarnab location (Table 4). The very
small linkage disequilibrium value reflected on the potential recombination in
the citrus canker bacterial population in the region, which must have direct Table 4: Diversity
parameters observed for citrus canker population from various locations of main
citrus nurseries of district Peshawar
Location |
Sample size |
Distinct MLGs detected |
Gene diversity |
Genotypic diversity |
Evenness index |
Linkage disequilibrium |
Hayatabad |
22 |
22 |
0.336 |
0.955 |
1.000 |
0.020 |
Malkandair |
6 |
5 |
0.099 |
0.778 |
0.930 |
0.159 |
Tarnab |
22 |
22 |
0.221 |
0.955 |
1.000 |
0.006 |
Overall Peshawar |
50 |
49 |
0.276 |
0.978 |
0.978 |
0.022 |
implications to disease
management and resistance exploitation at the fruit orchards level.
Fig. 4: Divergence
among citrus canker population from various citrus host types sampled at
Peshawar, as revealed by Principal component analyses (A) and Principal co-ordinate analyses (B)
Divergence
and diversity across various citrus host types
To assess the role of host on divergence among citrus canker bacterial
isolates, both principal component analyses and principal coordinate analyses
were conducted, using information on host of origin of the samples, considering
their genotypic profile over the 35 RAPD loci. In the principal component
analyses, the first component contributed (11.37%) while second Table 5: Diversity
parameters observed for citrus canker population from various citrus host types
sampled at Peshawar
Population |
Sample size |
Distinct MLGs detected |
Gene diversity |
Genotypic diversity |
Evenness index |
Linkage disequilibrium |
Sour Orange |
17 |
16 |
0.282 |
0.934 |
0.969 |
0.059 |
Sweet Orange |
29 |
29 |
0.264 |
0.966 |
1.000 |
0.013 |
Eureka Lemon |
4 |
4 |
0.281 |
0.750 |
1.000 |
0.000 |
Overall population |
50 |
49 |
0.276 |
0.978 |
0.978 |
0.022 |
components contributed (9.83%) with an overall component contribution was
21.2%, however, no clear divergence was evident for host of origin (Fig 4A).
Isolates from various hosts were dispersed together on the principal component
analyses. This was further supported by the principal coordinate analysis,
where no clear groups were detected, and all the citrus canker bacterial
samples were dispersed having overlap with one another (Fig. 4B). The neighbour joining
phylogenetic tree was constructed considering information on host of origin,
which revealed the lack of such adivergence due to host among
citrus canker bacterial population from various citrus host types sampled at
Peshawar (Fig. 5A). Samples originated from various hosts were equally
dispersed across various phylogenetic clades on the phylogenetic tree. The lack of host dependent
population subdivision was further confirmed by the network analyses, where
samples originated from multiple hosts were dispersed across the network and
none of the part was specific to a given host in the network analyses conducted
based on 35 RAPD loci (Fig. 5B).
To assess whether a single or
few host specific lineages are prevalent on various citrus host, or diverse
lineages can grow on different citrus hosts, diversity parameters were assessed
for samples grouped as their host of origin. High diversity was observed for
the citrus canker population from various citrus host types sampled at Peshawar
(Table 5). Every citrus host represented a diverse set of multilocus genotypes i.e.,
49 MLGs were observed out of 50 genotyped samples. The genotype diversity
ranged from 0.750 (for Unika Lemon) to 0.966 (for sweet orange) with an average
of 0.978, while maximum gene diversity was detected for samples from sour
orange (0.282) and minimum was detected for samples from sweet orange (0.264)
with an overall diversity of 0.276, respectively. The maximum linkage
disequilibrium (0.059) was observed for sour orange whereas the minimum linkage
disequilibrium was observed for Unika Lemon (0.000).
Fig. 5: Divergence
among citrus canker population from various citrus host types sampled at
Peshawar, as revealed by Neighbor-joining (NJ) tree (A) and Network Analyses (B)
Discussion
Citrus canker
Disease incidence and severity remains variable due to differences in
environmental condition in pathogen survival (Honger et al. 2016). The
similar variations were observed in the current study (Strayer et al.
2016). The detection of genetic differences on the basis of molecular markers
provides fast and more detailed results as compared to other methods (Simoes et
al. 2007).
The selected marker confirmed its suitability for the
detection of diversity and divergence in citrus population. In our research, we
detected a high level of polymorphism and also detected 35 loci overall with an
average of 8.7 bands per loci. Our current study was in accordance with the
results of Katkar et al. (2016) who studied the diversity among the
isolates of Xac pv. citri collected from different agro-climate regions
of India. Larrea et al. (2018) studied Xanthomanas
species of different plants by using type 3 secretion systems. These isolates
were grouped together on the basis of different geographical location and with
limited genetic differences. Kharde et al. (2018) collected different isolates
of X. axonopodis from different places in Maharashtra state, India and
used morphological, biochemical and RAPD based analysis. They detected 100%
polymorphism on the basis of both RAPD and ISSR markers.
Diversity was higher
across all sampling locations as revealed by different diversity indices. Gadhe et
al. (2016) detected high genetic variability across multiple geographical
locations. Variable diversity across location would reflect on the differential
potential of adaptation of the pathogen to host resistance and disease
management strategy (Ali et al. 2014).
The high diversity was
accompanied by an overall lack of strong linkage disequilibrium, which reflects
on the potential role of recombination in these bacteria. Contrary to this
study, Ngoc et al. (2007) detected significant level of linkage
disequilibrium among molecular markers loci, suggesting absence of frequent
genetic exchange in the bacterial populations they studied. This result would
have a direct implication for disease management, as higher recombination would
enable rapid adaptation of pathogen strains to host resistance (Ali et al.
2014).
Divergence of isolates sampled
from different locations was present albeit weak, as assessed through principal
component analysis, principal coordinate analysis, neighbor joining tree and
network analysis. These analyses showed
that there was a weak pattern of divergence and the samples were equally
distributed across locations. Cuberto and Graham (2002), reported some distinct
isolates of Xanthomonas from some restricted areas in Malaysia and China
which were grouped separately from the rest of canker isolates using PCR
fingerprinting techniques and also showed similarity with a few diverse samples
infecting in Florida. Considering, the distribution of isolates on principle
component and principle coordinate analyses, the
bacterial strains of all three locations were not clustered in separate groups,
but rather had a dispersed assignment to three clusters. Similar results were
obtained in southeastern Nigeria strains where four bacteria were not clustered
on the basis of PCA (Ogunjobi 2006). Analyzed 50 bacterial strains and their
similarity based on the principal components and coordinate analysis showed
that clearly separated in to two components.
While
analysing the population structure due to host, a lack of host dependent
population subdivision was confirmed by the PCA, PCoA, phylogenetic tree and
network analyses, where in samples originated from multiple host,
no host specific clusters were identified (Fig. 3B). This is an interesting
result, suggesting that the pathogen can cross inoculate various host types and
thus overcome the host resistance (Shehzadi and Naz 2019; Patane et al.
2019). Host specific lineages have been reported for pathogens in various
crops, particularly the fungal pathogens like rice blast fungi (Gladieux et
al. 2018).
Interestingly,
diversity assessment for isolates originating on various host revealed that not
a single or few host specific lineages were
prevalent on different citrus host types, but rather a diverse population were
prevalent on different citrus hosts. This could be the result of high
recombination in a diverse population (Ali et al. 2014), which results
in independent evolution of pathogen variants to acquire virulence against
different host species.
Our results on diversity and divergence detected for
isolates sampled on various hosts revealed high diversity on all the citrus
host species, while the divergence was absent across different host types. The
study based on host specific and location specific population genetic structure
seem to be complementary to one another and also informative to draw the
genetic structure of Xac pv. citri.
The information generated from the current findings would be useful for
understanding molecular mechanism of pathogenicity and devising a better
disease management strategy.
Conclusion
From the findings of the study, it can be concluded that divergence
across host was absent. The overall
high diversity and very small linkage disequilibrium revealed a potential role
of recombination in the population. Future disease management must consider this high diversity and
recombination in the pathogen population. Future studies must be made to assess the diversity divergence across the
province and country with more robust sampling.
Acknowledgements
The work
received resources from the project awarded by the US Department of
Agriculture, Agricultural Research Service, under agreement No. 58-0206-0-171
F.
Author Contributions
The study was
designed by MA, MZ, IJ and SA. Surveillance and Sampling was done by SU, LJ, ZR
and MRK. Bacterial isolation and characterization was
done by SU, LJ and MA. Molecular Genotyping was done by SU, LJ, ZR, AI and MNK.
Population genetics analyses were done by SU, LJ and SA. Resources for the
study were provided by MA, MRK, IJ and SA. The manuscript was written by SU,
LJ, AI, MZ, MNK and SA. All authors revised and approved the manuscript.
Conflict of interest
The authors declare that they have no conflict of interest.
Data Availability
The data will be made avaialble on requests to the corresponding author.
Ethics Approval
Not applicable.
References
Ali MR, MF
Hasan, RS Lia, A Akter, MSE Sumi, MF Hossain, B Sikdar (2017). Isolation and
characterization of a canker disease causing pathogen from Citrus aurantifolia and evaluation of its biological control
measure. J Entomol Zool Stud 5:1526‒1532
Ali S, P
Gladieux, M Leconte, A Gautier,
AF Justesen, MS Hovmøller, J Enjalbert, CD Vallavieille-Pope (2014).
Origin, migration routes and worldwide population genetic structure of the
wheat yellow rust pathogen Puccinia
striiformis f. spp. tritici. PLoS Pathog
10; Article
e1003903
Alvarez A, A
Benedict, C Mizumoto, L Pollard, E Civerolo (1991). Analysis of Xanthomonas campestris pv. citri and X. c. citrumelo with monoclonal antibodies. Phytopathology 81:857‒865
Araujo EFD, LPD Queiroz, MA Machado (2003). What is citrus?
Taxonomic implications from a study of cp-DNA evolution in the tribe Citreae
(Rutaceae subfamily Aurantioideae). Org Divers Evol 3:55‒62
Brunings AM and DW Gabriel (2003). Xanthomonas
citri: Breaking the surface. Mol
Plant Pathol 4:141‒157
Civerolo E (1984).
Bacterial canker disease of citrus (Xanthomonas
campestris). J Rio Grand Vall Hortic
Assoc 37:127‒146
Cuberto J, JH Graham (2002). Genetic relationship among worldwide strains
of Xanthomonas causing canker in
citrus species and design of new primers. Appl
Environ Microbiol 68:1257–1264
Das A (2003).
Citrus canker-A review. J Appl Hortic 5:52‒60
Graham JH, M Dewdney (2014). Brown rot of fruit. In: Florida citrus pest management guide, pp:67–68. Lake alfred, university of FloridaGadhe SK, SH
Antre, BB Ghorpade, RH Autade, RR Mandlik (2016). Studies on molecular
variability among Xanthomonas axonopodis pv. punicae isolates collected from Different Locations. Intl J Pure Appl Biosci 4:160‒166
Gladieux P, B
Condon, S Ravel, D Soanes, JL Maciel, A Nhani, L
Chen, R Terauchi, MH Lebrun, D Tharreau, T Mitchell, KF Pedley, B Valent, NJ Talbot, M Farman, E Fournier (2018). Gene flow between divergent cereal-and
grass-specific lineages of the rice blast fungus Magnaporthe oryzae. Amer Soc Microbiol 9; Article e01219-17
Gottwald TR,
JH Graham, TS Schubert (2002). Citrus canker: The pathogen and its impact. Plant Health Progr
3:15–48
Gottwald TR, A Alvarez, J Hartung, A Benedict (1991). Diversity of Xanthomonas campestris pv. citrumelo
strains associated with epidemics of citrus bacterial spot in Florida citrus
nurseries: Correlation of detached leaf, monoclonal antibody, and restriction
fragment length polymorphism assays. Phytopathology
81:749‒753
Graham J, T
Gottwald, T Riley, J Cubero, D Drouillard (2000). Survival of Xanthomonas campestris pv. citri (Xcc)
on various surfaces and chemical control of Asiatic citrus canker (ACC). In:
Proceedings of the Intern. Citrus Canker Research Workshop, Florida. June 20–22, 2000, Ft. Pierce, Florida, USA
Honger JO, E
Essuman, EW Cornelius (2016). The Incidence, severity and etiology of a
bacterial canker disease of citrus in Ghana. West Afr J Appl Ecol 24:31‒44
Kahn T, R
Krueger, D Gumpf, M Roose, ML Arpaia, T Batkin, S Cockerham (2001). Citrus genetic resources in california: analysis and recommendations for long-term
conservation. Report of the Citrus
Genetic Resources Assessment Task Force. Division of Agriculture and
Natural Resources, University of California, Davis, California, USA
Katkar M, KS
Raghuwanshi, VP Chimote, SG Borkar (2016). Pathological, Bio-chemical and
Molecular diversity amongst the isolates of Xanthomonas
axonopodis pv. citri causing citrus canker in acid lime from different
agro-climatic region of India. Intl J
Environ Agric Biotech 1; Article 1.2.25
Kharde RR, SA
Lavale, BB Ghorpade (2018). Molecular diversity among the isolates of Xanthomonas axonopodis pv. citri causing bacterial canker in citrus. Intl J Curr Microbiol Appl Sci 7:2375‒2384
Larrea SA, U Dhakal, G
Boluk, L Fatdal, A Alvarez, A
Strayer-Scherer, M Paret, J Jones, D
Jenkins, M Arif (2018). Development of a genome-informed
loop-mediated isothermal amplification assay for rapid and specific detection
of Xanthomonas euvesicatoria. Sci Rep 8; Article 14298
Leyns F, MD Cleene, JG Swings, JD
Ley (1984). The host range of the genus Xanthomonas.
Bot Rev 50:308‒356
Memon N (2017). Citrus fruit (Kino). Exclusive on Kino. Pak Food J 7:29‒31
Ngoc LBT, C Vernière, O Pruvost, N Kositcharoenkul, S Phawichit (2007). First report in Thailand of Xanthomonas axonopodis pv. citri-A* causing citrus canker on lime. Plant Dis 91:771‒771
Ogunjobi AA (2006). Molecular variation in population structure
of Xanthomonas axonopodis pv manihotis
in the south eastern Nigeria. Afr J Biotechnol 5:1868‒1872
Patane JS, J
Martins, LT Rangel, J Belasque, LA Digiampietri, AP Facincani, NF Almeida (2019).
Origin and diversification of Xanthomonas
citri subspp. citri pathotypes
revealed by inclusive phylogenomic, dating, and biogeographic analyses. BMC Genomics 20; Article 700
Pruvost O, JS Hartung, EL Civerelo, C Dubois, X Perrier (1992). Plasmid
DNA fingerprinting distinguished pathotypes of Xanthomanas compestris. J.
Phytopathol 82:485‒490
Schaad NW, JB
Jones, W Chun (2001). Laboratory Guide
for the Identification of Plant Pathogenic Vacteria,
3rd edn. American Phytopathology Society, Saint
Paul, Minnesota, USA
Schubert TS, JW
Miller (1996). Bacterial citrus canker Fla. Department Agric and Consumer Services, Division of Plant
Industry, Canberra, Australia
Shehzadi I, S
Naz (2019). Morphological, biochemical and genetic characterization of citrus
canker pathogen (Xanthomonas axonopodis)
from citrus cultivars of Punjab, Pakistan. J
Anim Plant Sci 29:117‒124
Siddique MI,
E Garnevska (2018). Citrus Value Chain(s): A survey of Pakistan citrus
industry. Agric Value Chain 26; Article 37
Silva ARD, JA
Ferro, FDC Reinach, CS Farah, LR Furlan, RB Quaggio, L Alves (2002). Comparison
of the genomes of two Xanthomonas
pathogens with differing host specificities. Nature 417:459‒463
Simoes TH, ER Gonçalves, YB Rosato, A Mehta (2007). Differentiation of Xanthomonas species by PCR-RFLP of rpf B
and atp D genes. FEMS Microbiol Lett
271:33‒39
Strayer AL, A Jeyaprakash, GV Minsavage, S Timilsina, GE Vallad, JB
Jones, ML Paret (2016). A multiplex
real-time PCR assay differentiates four Xanthomonas
species associated with bacterial spot of tomato. Plant Dis 100:1660‒1668
Sun X, RE
Stall, JB Jones, J Cubero, TR Gottwald, JH Graham, VK Stromberg (2004).
Detection and characterisation of a new strain of citrus canker bacteria from
Key/Mexican lime and alemow in South Florida. Plant Dis 88:1179‒1188
Ulubelde M (1985).
Turunçgillerin taksonomisi. Ege Bölg Zir Arast
Enst Yayınl 55:43
Vernière C, J Hartung, O Pruvost, E Civerolo, AM Alvarez, P Maestri, J
Luisetti 1998. Characterization of phenotypically distinct strains of Xanthomonas axonopodis pv. citri from Southwest Asia. Eur J Plant Pathol 104:477‒487